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hbond_sr_bb and hbond_lr_bb for different chains

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hbond_sr_bb and hbond_lr_bb for different chains

In the rosetta scoring function, what energy term describes backbone-backbone hydrogen bonding between residues on different protein chains

hbond_sr_bb                                Backbone-backbone hbonds close in primary sequence.  All hydrogen bonding terms support canonical and noncanonical types.
hbond_lr_bb                                Backbone-backbone hbonds distant in primary sequence.


Do the above terms only specify hydrogen bonding on a single chain? (as they are stratified by distance in primary sequence)



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Tue, 2020-10-13 13:41

The hbond_sr_bb type is intended for alpha helical hydrogen bonds, and is only active if you're on the same chain and within a short (less than 4 or so) distance of the other residue.

The hbond_lr_bb is intended for beta sheets (and other), and does not have a chain dependence. Two beta strands making hydrogen bonds with identical geometries will score the same whether the strands are in the same chain or are split between chains.

(The rationale for the difference is because Rosetta tends to really like forming alpha helicies because they're easy to find with a local structural search, versus beta strand pairings, which need a more global search. It was found that specifically downweighting the alpha helical hydrogen bonds tended to help counteract that bias with older scorefunctions. Recent scorefunctions, though, have a sightly different overall weighting scheme, and it's been found that there is no longer a need to weight the terms differently. They're still listed separately, but in the Talaris and REF energy functions all of the backbone hydrogen bonds have identical weights.)

Wed, 2020-10-14 08:25

Excellent thanks!

Tue, 2021-02-09 16:33